Browse Rfam families with structures

Rfam includes 167 families with three-dimensional structures. The table may be sorted by clicking on the column titles, or restored to the original order here. Please note that sorting large tables can be slow. Go back to the browse index.

0 - 9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Original order ID Accession Type Seed Full Number of structures Description
0 2dG-I RF01510 Cis-reg; riboswitch; 4 24 16 2dG-I riboswitch aptamer (M. florum)
1 5S_rRNA RF00001 Gene; rRNA; 712 594,154 2220 5S ribosomal RNA
2 5_8S_rRNA RF00002 Gene; rRNA; 61 16,501 1466 5.8S ribosomal RNA
3 6S RF00013 Gene; 150 5,006 1 6S / SsrS RNA
4 7SK RF00100 Gene; 45 49,373 13 7SK RNA
5 abiF RF03085 Gene; sRNA; 126 282 2 abiF RNA
6 ACEA_U3 RF01848 Gene; snRNA; snoRNA; CD-box; 28 2,156 11 ACEA small nucleolar RNA U3
7 AdoCbl-II RF01689 Cis-reg; riboswitch; 146 174 33 AdoCbl-II (Cobalamin/B12) riboswitch aptamer
8 Archaea_SRP RF01857 Gene; 54 294 1 Archaeal signal recognition particle RNA
9 ARRPOF RF02933 Gene; sRNA; 35 1 4 ARRPOF RNA
10 azaaromatic RF01764 Cis-reg; riboswitch; 62 445 10 azaaromatic riboswitch aptamer (yjdF RNA)
11 Bacteria_large_SRP RF01854 Gene; 92 1,447 5 Bacterial large signal recognition particle RNA
12 Bacteria_small_SRP RF00169 Gene; 261 6,888 21 Bacterial small signal recognition particle RNA
13 c-di-AMP RF00379 Cis-reg; riboswitch; 106 7,607 16 c-di-AMP riboswitch aptamer (ydaO/yuaA leader)
14 c-di-GMP-I RF01051 Cis-reg; riboswitch; 155 5,092 17 c-di-GMP-I riboswitch aptamer
15 c-di-GMP-I-GGC RF03167 Cis-reg; riboswitch; 40 1,298 11 c-di-GMP-I-GGC riboswitch aptamer
16 c-di-GMP-II RF01786 Cis-reg; riboswitch; 54 541 2 Cyclic di-GMP-II riboswitch aptamer
17 Cobalamin RF00174 Cis-reg; riboswitch; 434 20,864 14 Cobalamin riboswitch aptamer
18 Corona_FSE RF00507 Cis-reg; frameshift_element; 51 76 8 Coronavirus frameshifting stimulation element
19 CPEB3_ribozyme RF00622 Gene; ribozyme; 14 5,706 3 Mammalian CPEB3 ribozyme
20 CRISPR-DR16 RF01330 Gene; CRISPR; 6 1,291 2 CRISPR RNA direct repeat element
21 CRISPR-DR22 RF01335 Gene; CRISPR; 9 463 1 CRISPR RNA direct repeat element
22 CRISPR-DR34 RF01344 Gene; CRISPR; 5 577 14 CRISPR RNA direct repeat element
23 CRISPR-DR4 RF01317 Gene; CRISPR; 33 15,411 4 CRISPR RNA direct repeat element
24 DENV_SLA RF02340 Cis-reg; 15 2 6 Dengue virus SLA
25 DnaX RF00382 Cis-reg; frameshift_element; 5 102 2 DnaX ribosomal frameshifting element
26 DUF2693-FD RF02926 Gene; sRNA; 92 5 1 DUF2693-FD RNA
27 Entero_5_CRE RF00386 Cis-reg; 160 1 11 Enterovirus 5' cloverleaf cis-acting replication element
28 Flavivirus_DB RF00525 Cis-reg; 112 13 2 Flavivirus DB element
29 Flavivirus_SLIV RF01415 Cis-reg; 21 0 1 Flavivirus 3'UTR stem loop IV
30 Flavi_CRE RF00185 Cis-reg; 84 6 2 Flavivirus 3' UTR cis-acting replication element (CRE)
31 Fluoride RF01734 Cis-reg; riboswitch; 289 2,293 6 Fluoride riboswitch aptamer (crcB RNA motif)
32 FMN RF00050 Cis-reg; riboswitch; 146 6,230 8 FMN riboswitch aptamer (RFN element)
33 Fungi_U3 RF01846 Gene; snRNA; snoRNA; CD-box; 66 1,319 49 Fungal small nucleolar RNA U3
34 Gammaretro_CES RF00374 Cis-reg; 25 81 2 Gammaretrovirus core encapsidation signal
35 GIR1 RF01807 Gene; ribozyme; 13 0 1 GIR1 branching ribozyme
36 glmS RF00234 Cis-reg; riboswitch; 18 1,328 39 glmS glucosamine-6-phosphate activated ribozyme aptamer
37 GlmY_tke1 RF00128 Gene; sRNA; 17 149 2 Glm Y RNA activator of glmS mRNA
38 GlmZ_SraJ RF00083 Gene; sRNA; 22 117 2 GlmZ RNA activator of glmS mRNA
39 Glutamine RF01739 Cis-reg; riboswitch; 940 272 6 Glutamine riboswitch aptamer (glnA leader)
40 Glutamine-II RF01704 Cis-reg; riboswitch; 628 59 2 Glutamine-II riboswitch aptamer
41 Glycine RF00504 Cis-reg; riboswitch; 44 9,425 25 Glycine riboswitch aptamer
42 GOLLD RF02032 Gene; 35 44 73 Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA
43 GP_knot1 RF01073 Cis-reg; 8 3,368 1 Gag/pol translational readthrough site
44 group-II-D1D4-1 RF01998 Intron; 237 2,508 57 Group II catalytic intron D1-D4-1
45 group-II-D1D4-3 RF02001 Intron; 406 4,274 67 Group II catalytic intron D1-D4-3
46 group-II-D1D4-7 RF02012 Intron; 244 1,296 6 Group II catalytic intron D1-D4-7
47 Guanidine-I RF00442 Cis-reg; riboswitch; 100 1,509 10 Guanidine-I riboswitch aptamer
48 Guanidine-III RF01763 Cis-reg; riboswitch; 41 1,282 13 Guanidine-III riboswitch aptamer (yKKC-III)
49 Hairpin-meta1 RF04190 Gene; ribozyme; 84 0 8 Hairpin ribozyme 1 from viruses-like metatranscriptomes
50 Hammerhead_1 RF00163 Gene; ribozyme; 29 324,155 2 Hammerhead ribozyme (type I)
51 Hatchet RF02678 Gene; ribozyme; 155 24 3 Hatchet ribozyme
52 HBV_epsilon RF01047 Cis-reg; 33 14 1 HBV RNA encapsidation signal epsilon
53 HCV_ARF_SL RF00620 Cis-reg; 57 1 3 Hepatitis C alternative reading frame stem-loop
54 HDV_ribozyme RF00094 Gene; ribozyme; 33 16 14 Hepatitis delta virus ribozyme
55 Histone3 RF00032 Cis-reg; 50 44,596 5 Histone 3' UTR stem-loop
56 HIV-1_DIS RF00175 Cis-reg; 70 29 10 Human immunodeficiency virus type 1 dimerisation initiation site
57 HIV-1_SD RF01380 Cis-reg; 22 53 3 Human immunodeficiency virus type 1 major splice donor
58 HIV-1_SL3 RF01381 Cis-reg; 19 25 1 HIV-1 stem-loop 3 Psi packaging signal
59 HIV_FE RF00480 Cis-reg; frameshift_element; 147 29 5 HIV Ribosomal frameshift signal
60 HIV_PBS RF00375 Cis-reg; 132 21 6 HIV primer binding site (PBS)
61 Intron_gpI RF00028 Intron; 12 5,602 55 Group I catalytic intron
62 Intron_gpII RF00029 Intron; 92 49,099 35 Group II catalytic intron
63 IRES_Cripavirus RF00458 Cis-reg; IRES; 18 19 17 Cripavirus internal ribosome entry site (IRES)
64 IRES_HCV RF00061 Cis-reg; IRES; 51 1 31 Hepatitis C virus internal ribosome entry site
65 IRES_HepA RF00228 Cis-reg; IRES; 23 0 2 Hepatitis A virus internal ribosome entry site (IRES)
66 IRES_Pesti RF00209 Cis-reg; IRES; 42 1 1 Pestivirus internal ribosome entry site (IRES) including 5'UTR SLI
67 IRES_Picorna_2 RF00210 Cis-reg; IRES; 92 12 4 Aphthovirus internal ribosome entry site (IRES)
68 IRE_I RF00037 Cis-reg; 62 6,829 2 Iron response element I
69 IRE_II RF02253 Cis-reg; 30 5,197 1 Iron response element II
70 K10_TLS RF00207 Cis-reg; 10 18 5 K10 transport/localisation element (TLS)
71 let-7 RF00027 Gene; miRNA; 64 8,694 9 let-7 microRNA precursor family
72 LSU_rRNA_archaea RF02540 Gene; rRNA; 91 2,955 2581 Archaeal large subunit ribosomal RNA
73 LSU_rRNA_bacteria RF02541 Gene; rRNA; 102 51,934 2743 Bacterial large subunit ribosomal RNA
74 LSU_rRNA_eukarya RF02543 Gene; rRNA; 88 107,465 2491 Eukaryotic large subunit ribosomal RNA
75 LSU_trypano_mito RF02546 Gene; rRNA; 6 12 12 Trypanosomatid mitochondrial large subunit ribosomal RNA
76 Lysine RF00168 Cis-reg; riboswitch; 47 3,224 16 Lysine riboswitch aptamer
77 Magnesium RF00380 Cis-reg; riboswitch; 159 1,095 3 M-box riboswitch aptamer (ykoK leader)
78 Manganese RF00080 Cis-reg; riboswitch; 29 1,126 4 Manganese Mn2+ riboswitch aptamer (yybP-ykoY)
79 mascRNA-menRNA RF01684 Gene; 53 1,900 12 MALAT1-associated small cytoplasmic RNA/MEN beta RNA
80 Metazoa_SRP RF00017 Gene; 91 383,523 19 Metazoan signal recognition particle RNA
81 mir-15 RF00455 Gene; miRNA; 164 2,045 3 mir-15 microRNA precursor family
82 mir-16 RF00254 Gene; miRNA; 14 4,705 3 mir-16 microRNA precursor family
83 mir-17 RF00051 Gene; miRNA; 234 4,687 1 mir-17 microRNA precursor family
84 mir-2985 RF02095 Gene; miRNA; 8 2,000 1 mir-2985 microRNA precursor family
85 mir-31 RF00661 Gene; miRNA; 75 1,181 1 mir-31 microRNA precursor family
86 mir-663 RF00957 Gene; miRNA; 6 102 3 mir-663 microRNA precursor family
87 mir-H11 RF04076 Gene; miRNA; 6 60 2 mir-H11 microRNA precursor family
88 mir-TAR RF00250 Gene; miRNA; 45 48 13 Trans-activation response element (TAR)
89 MIR166 RF00075 Gene; miRNA; 31 2,599 1 mir-166 microRNA precursor family
90 MS2 RF02359 Cis-reg; 5 3 1 Bacteriophage MS2 operator hairpin
91 msr RF00170 Gene; 7 18 13 Retron msr RNA
92 nadA RF03013 Gene; sRNA; 186 48 16 nadA riboswitch
93 NiCo RF02683 Cis-reg; riboswitch; 83 215 1 NiCo (Nickel/Cobalt) riboswitch aptamer
94 OLE RF01071 Gene; 20 445 4 Ornate Large Extremophilic RNA
95 Pab160 RF02796 Gene; snRNA; snoRNA; HACA-box; 5 2 6 Pab160 RNA
96 Phage_DGR RF03022 Gene; sRNA; 114 3 9 Bacteriophage Diversity-Generating Retroelement RNA
97 Phage_pRNA RF00044 Gene; 5 1 15 3WJ core of Phi29 Bacteriophage pRNA
98 Pistol RF02679 Gene; ribozyme; 47 61 13 Pistol ribozyme
99 preQ1-II RF01054 Cis-reg; riboswitch; 15 49 1 PreQ1-II (pre queuosine) riboswitch aptamer
100 PreQ1-III RF02680 Cis-reg; riboswitch; 31 10 5 PreQ1-III (pre queuosine) riboswitch aptamer
101 Protozoa_SRP RF01856 Gene; 18 111 17 Protozoan signal recognition particle RNA
102 PrrB_RsmZ RF00166 Gene; sRNA; 39 84 4 PrrB/RsmZ RNA family
103 Purine RF00167 Cis-reg; riboswitch; 133 4,097 75 Purine riboswitch aptamer
104 PV_xrRNA_class3 RF04326 Cis-reg; 354 80 2 Exoribonuclease-resistant RNA (xrRNA) plant-infecting virus (class 3)
105 RAGATH-18 RF03064 Gene; sRNA; 1,420 518 1 RAGATH-18 RNA
106 raiA RF03072 Cis-reg; riboswitch; 488 489 6 raiA RNA
107 RNA-OUT RF00240 Gene; antisense; 16 102 1 RNA-OUT
108 RNAI RF00106 Gene; antisense; 10 156 2 RNAI
109 RNaseP_arch RF00373 Gene; ribozyme; 70 295 4 Archaeal RNase P
110 RNaseP_bact_a RF00010 Gene; ribozyme; 458 8,471 8 Bacterial RNase P class A
111 RNaseP_bact_b RF00011 Gene; ribozyme; 114 955 4 Bacterial RNase P class B
112 RNaseP_nuc RF00009 Gene; ribozyme; 116 3,848 4 Nuclear RNase P
113 RNase_MRP RF00030 Gene; ribozyme; 66 3,510 5 RNase MRP
114 ROOL RF03087 Gene; sRNA; 290 39 64 ROOL RNA
115 RRE RF00036 Cis-reg; 65 34 1 HIV Rev response element
116 RT-12 RF03016 Gene; sRNA; 42 15 2 RT-12 RNA
117 RydC RF00505 Gene; sRNA; 6 23 1 RydC RNA
118 S15 RF00114 Cis-reg; leader; 78 727 2 Ribosomal S15 leader
119 s2m RF00164 Cis-reg; 39 22 1 Coronavirus 3' stem-loop II-like motif (s2m)
120 SAH RF01057 Cis-reg; riboswitch; 52 1,354 3 SAH (S-adenosyl-L-homocysteine) riboswitch aptamer
121 salivarius-1 RF03030 Gene; sRNA; 20 5 2 salivarius-1 RNA
122 SAM RF00162 Cis-reg; riboswitch; 457 9,625 29 SAM riboswitch aptamer (S box leader)
123 SAM-I-IV RF01725 Cis-reg; riboswitch; 417 567 2 SAM-I/IV (S-adenosyl methionine) riboswitch aptamer
124 SAM-IV RF00634 Cis-reg; riboswitch; 40 2,360 4 SAM (S-adenosyl methionine) riboswitch aptamer
125 SAM-SAH RF01727 Cis-reg; riboswitch; 54 364 1 SAM/SAH riboswitch aptamer
126 SAM_V RF01826 Cis-reg; riboswitch; 7 23 1 SAM-V (S-adenosyl methionine) riboswitch aptamer
127 Sarbecovirus-5UTR RF03120 Cis-reg; 19 8 2 Sarbecovirus 5'UTR
128 SECIS_1 RF00031 Cis-reg; 61 3,793 2 Selenocysteine insertion sequence 1
129 snR30 RF01271 Gene; snRNA; snoRNA; HACA-box; 5 23 2 Small nucleolar RNA snR30
130 SSU_rRNA_archaea RF01959 Gene; rRNA; 86 709 2379 Archaeal small subunit ribosomal RNA
131 SSU_rRNA_bacteria RF00177 Gene; rRNA; 99 42,628 2443 Bacterial small subunit ribosomal RNA
132 SSU_rRNA_eukarya RF01960 Gene; rRNA; 90 75,755 2366 Eukaryotic small subunit ribosomal RNA
133 SSU_rRNA_microsporidia RF02542 Gene; rRNA; 46 1,035 2383 Microsporidia small subunit ribosomal RNA
134 SSU_trypano_mito RF02545 Gene; rRNA; 4 11 17 Trypanosomatid mitochondrial small subunit ribosomal RNA
135 TCV_H5 RF00500 Cis-reg; 5 1 1 Turnip crinkle virus (TCV) repressor of minus strand synthesis H5
136 Telomerase-cil RF00025 Gene; 21 4 6 Ciliate telomerase RNA
137 Telomerase-vert RF00024 Gene; 37 523 20 Vertebrate telomerase RNA
138 THF RF01831 Cis-reg; riboswitch; 101 747 12 THF (Tetrahydrofolate) riboswitch aptamer
139 THF-II RF02977 Cis-reg; 46 67 16 THF-II riboswitch (folE RNA)
140 TLS-PK3 RF01084 Cis-reg; 9 14 7 Pseudoknot of tRNA-like structure
141 tmRNA RF00023 Gene; 477 8,092 24 transfer-messenger RNA
142 tmRNA_permuted RF04321 Gene; 296 1,734 9 permuted transfer-messenger RNA
143 ToxI RF02519 Gene; antitoxin; 5 1 1 ToxI antitoxin
144 TPP RF00059 Cis-reg; riboswitch; 115 16,130 38 TPP riboswitch aptamer (THI element)
145 tracrRNA RF02348 Gene; CRISPR; 37 41 37 Trans-activating crRNA
146 tRNA RF00005 Gene; tRNA; 954 5,335,975 3345 tRNA
147 tRNA-Sec RF01852 Gene; tRNA; 109 4,211 37 Selenocysteine transfer RNA
148 Twister-sister RF02681 Gene; ribozyme; 113 17 5 Twister_sister_ribozyme
149 Tymo_tRNA-like RF00233 Cis-reg; 29 38 3 Tymovirus/Pomovirus/Furovirus tRNA-like 3' UTR element
150 TYMV_upPK RF00390 Cis-reg; 7 3 2 turnip yellow mosaic virus upstream pseudo-knot (TYMV_upPK)
151 U1 RF00003 Gene; snRNA; splicing; 100 40,184 11 U1 spliceosomal RNA
152 U11 RF00548 Gene; snRNA; splicing; 72 2,595 7 U11 spliceosomal RNA
153 U12 RF00007 Gene; snRNA; splicing; 62 2,106 2 U12 minor spliceosomal RNA
154 U1_yeast RF00488 Gene; snRNA; splicing; 5 27 8 Yeast U1 spliceosomal RNA
155 U2 RF00004 Gene; snRNA; splicing; 208 71,512 93 U2 spliceosomal RNA
156 U3 RF00012 Gene; snRNA; snoRNA; CD-box; 87 19,072 13 Small nucleolar RNA U3
157 U4 RF00015 Gene; snRNA; splicing; 177 32,178 33 U4 spliceosomal RNA
158 U4atac RF00618 Gene; snRNA; splicing; 61 1,648 1 U4atac minor spliceosomal RNA
159 U5 RF00020 Gene; snRNA; splicing; 180 28,527 102 U5 spliceosomal RNA
160 U6 RF00026 Gene; snRNA; splicing; 188 204,442 104 U6 spliceosomal RNA
161 U6atac RF00619 Gene; snRNA; splicing; 62 9,067 2 U6atac minor spliceosomal RNA
162 U7 RF00066 Gene; snRNA; 49 10,439 5 U7 small nuclear RNA
163 VA RF00102 Gene; 55 40 1 VA RNA
164 Virus-PTE RF02521 Cis-reg; 3 1 1 Panicum mosaic virus cap-independent translation enhancer RNA (PTE)
165 Xanthine RF03054 Cis-reg; riboswitch; 383 275 9 Xanthine riboswitch aptamer (NMT1 RNA)
166 ZMP-ZTP RF01750 Cis-reg; riboswitch; 185 3,295 17 ZMP/ZTP riboswitch aptamer (pfl RNA motif)
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